GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Pedobacter sp. GW460-11-11-14-LB5

Align UDP-glucose 4-epimerase; EC 5.1.3.2 (characterized, see rationale)
to candidate CA265_RS25430 CA265_RS25430 UDP-glucose 4-epimerase GalE

Query= uniprot:L0FXG3
         (337 letters)



>FitnessBrowser__Pedo557:CA265_RS25430
          Length = 340

 Score =  364 bits (935), Expect = e-105
 Identities = 183/338 (54%), Positives = 238/338 (70%), Gaps = 4/338 (1%)

Query: 1   MQQILITGGAGYIGSHTAVALVNAGYEPIIVDNFSNSNKEVLNGLEKILGAPVKYHEGDC 60
           M +IL+TGG GYIGSHTAV L NAGYE +IVDN SNSN ++L  L  I G    +HE D 
Sbjct: 1   MAKILVTGGTGYIGSHTAVELHNAGYEVVIVDNLSNSNIKILTQLHAITGKWFDFHEIDL 60

Query: 61  NDRKFMQAVFEEN-DLQGVIHFAASKAVGESTKIPLTYYSNNINSLIILLETMKQFGVKD 119
            D + +Q   E + D+ G+IHFAASKAVGES + PL YY NN   LI LL +  +    +
Sbjct: 61  QDDRAVQEFAENHTDIDGIIHFAASKAVGESVEQPLKYYKNNFYGLINLLTSFNR--KIN 118

Query: 120 IVFSSSCTVYGQPDKLPVKETTPRKDAESPYGNTKKICEDILTDHVKSGAPARVVALRYF 179
            VFSSSCTVYGQP+ LPV E  P + AESPYGNTK+I E+IL +         ++ALRYF
Sbjct: 119 FVFSSSCTVYGQPETLPVTEAAPVQKAESPYGNTKQIAEEILAETAAVTPALNIIALRYF 178

Query: 180 NPIGAHPSSLIGELPLGVPANLIPFVTQTGAGIREKITVFGDDYNTPDGTCIRDYIHVMD 239
           NP+GAH ++LIGELP GVPANL+PF+TQ+  G R  ITV+GDDY+TPDG+ IRDYIHV+D
Sbjct: 179 NPVGAHETALIGELPNGVPANLVPFITQSAIGKRGPITVYGDDYDTPDGSAIRDYIHVVD 238

Query: 240 LADAHVKSIQYLAD-QPENFIDLFNVGTGNGNTVMEVIKAFEKVSEKPLNYEIGPRRSGD 298
           LA AHV +I+ L +  P    D+FN+GTG G++V+E+I AFEKV+ + L+Y+IGPRR+GD
Sbjct: 239 LAKAHVAAIKKLEEGNPNGNYDVFNIGTGKGSSVLEIIAAFEKVNGEKLDYKIGPRRAGD 298

Query: 299 IEKVWANTDKVSKVLGWTPQFGLEEALRDAWNWQLSLK 336
           I +++ +  K +  LGW     + E +R AW W+  +K
Sbjct: 299 IVQIYGDVQKSNNELGWKANLDINEMMRSAWEWEKYIK 336


Lambda     K      H
   0.316    0.136    0.403 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 398
Number of extensions: 18
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 337
Length of database: 340
Length adjustment: 28
Effective length of query: 309
Effective length of database: 312
Effective search space:    96408
Effective search space used:    96408
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate CA265_RS25430 CA265_RS25430 (UDP-glucose 4-epimerase GalE)
to HMM TIGR01179 (galE: UDP-glucose 4-epimerase GalE (EC 5.1.3.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.29872.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.29872.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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